6NLA

Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Design of High-Affinity Metal-Controlled Protein Dimers.

Maniaci, B.Lipper, C.H.Anipindi, D.L.Erlandsen, H.Cole, J.L.Stec, B.Huxford, T.Love, J.J.

(2019) Biochemistry 58: 2199-2207

  • DOI: https://doi.org/10.1021/acs.biochem.9b00055
  • Primary Citation of Related Structures:  
    6NL6, 6NL7, 6NL8, 6NL9, 6NLA, 6NLB

  • PubMed Abstract: 

    The ability to precisely control protein complex formation has high utility in the expanding field of biomaterials. Driving protein-protein binding through metal-ligand bridging interactions is a promising method of achieving this goal. Furthermore, the capacity to precisely regulate both complex formation and dissociation enables additional control not available with constitutive protein complexes. Here we describe the design of three metal-controlled protein dimers that are completely monomeric in the absence of metal yet form high-affinity symmetric homodimers in the presence of zinc sulfate. The scaffold used for the designed dimers is the β1 domain of streptococcal protein G. In addition to forming high-affinity dimers in the presence of metal, the complexes also dissociate upon addition of EDTA. Biophysical characterization revealed that the proteins maintain relatively high thermal stability, bind with high affinity, and are completely monodisperse in the monomeric and dimeric states. High-resolution crystal structures revealed that the dimers adopt the target structure and that the designed metal-binding histidine residues successfully bind zinc and function to drive dimer formation.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G56StreptococcusMutation(s): 7 
Gene Names: spg
UniProt
Find proteins for P19909 (Streptococcus sp. group G)
Explore P19909 
Go to UniProtKB:  P19909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19909
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.155α = 90
b = 63.155β = 90
c = 39.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Structure summary
  • Version 1.3: 2023-05-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description